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Thank you to all who joined and participated in the HUPO ECR Panel Discussion on Translating Science from Benchtop to Biotech on August 9, 2023.

This panel is part of a seminar series organized by the HUPO Early Career Researcher Committee and The Young Proteomics Investigators Club (YPIC). These panels offer a space to foster professional development by engaging with the community. This time, two delightful panelists provided their time and expertise: Ruedi Aebersold (Co-founder of Biognosys) and Jarrod Sandow (Director and Senior Scientist at IonOpticks).

They commented on important considerations about scientific entrepreneurship such as intellectual property. Attendees learned about the resources often available within institutes or at incubators to refine a business plan . All in all this panel session highlighted the interesting opportunities of commercializing science, which can take the shape of a product, a service or developing proteomics technology. Thank you to our panelists and everyone that participated and made this such a great event.

Stay tuned for upcoming panel sessions!

The August HUPOST is now available featuring important congress information, next ECR webinar, ECR competition finalists, HUPO member notices, C-HPP workshop and more!

The HUPO ECR Committee is delighted to showcase the finalists of the 9th annual edition of the Manuscript Competition - take a look at their short bios below:

Dr. Johannes Bruno Müller-Reif
Max Planck Institute Of Biochemistry, Germany

Dr. Johannes Bruno Müller-Reif is a project leader and head of the Pediatric Proteomics Group at the Max Planck Institute of Biochemistry (MPIB). During his doctorate with Prof. Matthias Mann he focused on extending proteomics across the tree of life. Following his PhD, he joined the proteomics start-up OmicEra, where he significantly contributed to high-throughput proteomics methods for biomarker discovery and clinical research. Concurrently, Dr. Müller-Reif maintained a relationship with MPIB as a guest scientist, and his growing expertise led him to establish a research group with focus on the intersection of mass spectrometry-based proteomics and pediatrics. Dr. Müller-Reif’s research is multifaceted. A cornerstone of his work involves applying mass spectrometry-based proteomics to large patient cohorts to enhance biomarker discovery. In this capacity, he co-leads the MOMI cohort’s plasma proteomics efforts to address adverse pregnancy outcomes, supported by the Bill and Melinda Gates Foundation. He also focuses on the utilization of proteomics for investigating rare pediatric diseases. Furthermore, Dr. Müller-Reif pioneers the use of proteomics in specialized applications such as platelet biology and studying organisms inaccessible through conventional methods. This innovative approach not only exemplifies the practical versatility of proteomics but also ties back to his doctoral research on the proteome landscape of the kingdoms of life.

Dr. Pavel Sinitcyn
Morgridge Institute For Research,  United States

Pavel Sinitcyn is a distinguished Morgridge Interdisciplinary Postdoctoral Fellow at UW-Madison, conducting cutting edge research in the Joshua Coon lab. With a strong background in developing software solutions for proteomics data processing, Pavel has played a pivotal role in developing tools such as MaxQuant, MaxDIA, Perseus, and Deep Proteomic Sequencing Method.

Prof. Hong Wang
Institute Of Hematology & Blood Diseases Hospital, Chinese Academy Of Medical Sciences & Peking Union Medical College, China

Hong Wang got his Ph.D degree in 2017 at the University of Tennessee Health Science Center/St Jude Children’s Hospital in USA. After a continuous postdoc training and senior scientist experience at St. Jude, he joined the institute of Hematology and Blood diseases hospital, Chinese Academy of Medical Sciences & Peking Union Medical College in 2021. He is now a professor of the National Key Laboratory of Blood Science and Founding Director of the Center for Advanced Technologies.

Dr. Wang has developed multiple cutting-edge Mass Spectrometry-based proteomics technologies enabling ultradeep whole proteomic profiling with sub-microgram materials. He also developed advanced bioinformatics pipelines for multi-omics integration. He has published several high impact research articles on prestigious journals as corresponding/first authors in the last five years, e.g. Immunity, Cancer Cell, Nature Communications, PNAS, Genome Biology and Molecular Neurodegeneration. His research interests including: 1, to develop high-throughput single-cell and single-cell type proteomics technologies;   2, to use advanced multi-omics integrative strategies to dissect the blood ecosystems in systematic diseases.

HUPO Early Career Researcher (ECR) Online Panel Webinar

DATE:  Wednesday, August 9, 2023
TIME:  9 am CEST (Central European Summer Time)
LOCATION:  Zoom
SPEAKERS:  Reudi Abersold (Co-founder of Biognosys) and Jarrod Sandow (Director and Senior Scientist at IonOpticks)

Want to learn about turning science into a business? Join us for the coming online panel discussion taking place on August 9 at 9 am CEST. This panel is part of a seminar series organized by the HUPO Early Career Researcher Committee and The Young Proteomics Investigators Club (YPIC). These seminars offer a space to foster professional development by engaging with the community. During this one-hour panel, we will hear on thoughts and views from experienced researchers on their involvement and trajectory in the establishment of successful biotechs! 

REGISTER HERE

DATE: Thursday, July 20, 2023
TIME: 11 am - 1330 pm EDT
LOCATION: Zoom

Exciting B/D-HPP webinar on aging and disease coming up. Join us and listen to diverse topics in aging and disease proteomics including cancer, Alzheimer’s disease, geroscience, and others.

PLEASE NOTE: All times listed below are Eastern Daylight Time (EDT).

1100 am EDT - ROGER REDDELL - Progress Towards Utilisation of Tissue Proteomics in the Cancer Clinic

1130 am EDT - RENA ROBINSON - High-throughput Proteomics Applications in Aging & Alzheimer’s Disease

1200 pm EDT - MAGGIE LAM - Post-transcriptional Regulation of Aging and Diseases

1230 pm EDT - BIRGIT SCHILLING - TBA

1300 pm EDT - NATHAN BASISTY - Leveraging Proteomics for Translational Geroscience

1330 pm EDT - Closing Remarks

REGISTER HERE

The manuscript competition is a unique opportunity for early career researchers to gain visibility in the proteomics community for their outstanding work. It serves as a platform to highlight the important contributions that postdoctoral fellows, young clinicians and junior faculty members make to the proteomics field.

Three finalists have been selected to present their publications in a dedicated plenary session at HUPO 2023 (in Busan), where an expert committee will evaluate the oral presentations to determine the “Proteomics Highlight of the Year”.

Congratulations to:

• Hong Wang, Institute of Hematology, Chinese Academy of Medical Sciences, Tianjin, China
• Pavel Sinitcyn, Morgridge Institute for Research, Madison, Wisconsin
• Johannes Mueller, Max Planck Institute of Biochemistry, Munich, Germany

The selection of exceptional manuscripts was a challenging task amongst many impressive submissions. The ECR would like to thank the careful evaluation and dedication from the judges: Wei Wu, Tiannan Guo, Jochen Schwenk, Ho Jeong Kwon, Concha Gil, Jennifer Geddes-McAlister, Yu-Ju Chen, Christian Moritz, Benjamin Garcia, Peter Hoffmann, Tadashi Kondo, Teck Yew Low, Fabio Nogueira, Stephen Pennington, Chantragan Phiphobmongkol, Anthony Purcell, Paola Roncada, Luis Manuel Teran, Olga Vitek, Juan Antonio Vizcaino, Marc Wilkins, Bernd Wollscheid, Shamshad Zarina and Qian Zhao! Thank you!

Open data practices in proteomics: the why, the how and the what for?

The goal of the ETC Auditorium "Stylish Academic Writing" professional development webinar series is to help students and trainees improve their scientific writing skills. The 5th webinar featured Dr. Juan Antonio Vizcaino, Proteomics Team Leader at the European Bioinformatics Institute (EMBL-EBI), as the lecturer. The discussion focused on the latest trends in open data practices in proteomics. Dr. Deepti Jaiswal Kundu, a Scientific Curator at the PRIDE database (EMBL-EBI) served as the host and Dr. Tiannan Guo, a Tenured Associate Professor at Westlake University, participated as a panelist.

This webinar focused on the advantages of open data sharing in proteomics and its potential to drive research, collaboration, and innovation. Dr. Vizcaino highlighted the importance of data repositories, such as PRIDE, MassIVE, JPOST, iProX, and Panorama, in facilitating open data sharing. The webinar emphasized the FAIR data principles (Findable, Accessible, Interoperable, and Re-usable) and encouraged researchers to contribute their proteomics data and promote collaboration within the scientific community. Inspiring examples of data re-use were showcased, along with the bottlenecks associated with utilizing public proteomics data, such as data complexity and lack of metadata annotation. The webinar stressed the significance of proper metadata documentation and introduced the Sample Description and Result Format (SDRF) file format to improve metadata annotation and enable meaningful re-use of proteomics data. Lastly, the challenges of data privacy, intellectual property rights, data standardization, and data curation were addressed, with strategies and recommendations provided to promote responsible and effective sharing of proteomics data.

Dr. Vizcaino also addressed some live questions (Q & A):

1.     Q:  How do you envision the future of the data repositories, knowing that data sets are now containing more and more samples, like single cells or instruments producing large data?

A:  It’s a continuous struggle that usually happens. We keep on innovating in terms of infrastructure in terms of keeping and dealing with large data. We take the experience /suggestions from other EBI repositories (e.g. those devoted to DNA/RNA sequencing data) about how they manage large datasets.

2.     Q:  The availability of sample metadata is crucial for identifying samples which are an important aspect of open data practices. A single large amount of data in PRIDE have metadata missing in them. So, what are your suggestions for the submitters in PRIDE.

A:  When ProteomeXchange started on that time the emphasis was put on data provision. But now it is more and more clear the necessity of more metadata. And that’s why the SDRF annotation has been proposed which is now promoted by PRIDE to submitters.

3.     Q:  Many journals have dedicated data availability sections where accessions are mentioned. Have you considered using these top detect publications with PRIDE id?

A:  We do that. We check the abstract of the publication and the full text (in the case of open-access journals).

4.     Q:  Are there any options in PRIDE to keep the RAW data private even if the article is public?

A:  The policy of ProteomeXchange is as soon as publication is out, the data needs to be public. There are some exceptional cases when data is sensitive like clinical data. We do not have any mechanism yet for the controlled access data but in the future, we might have to include it.

5.  Q:  Some data can be re-used, do you have suggestions on what type of data has been re-used?

A:  Datasets that are re-used the most are the ones that are more scientifically relevant, e.g. those published in high-profile journals. A second criterium includes those which are annotated better, where people don’t have to work on those.

A full video recording of the session including the talk and Q&A session is available on the HUPO YouTube channel website (https://www.hupo.org/Webinars-and-Virtual-Presentations).

For those with no access to YouTube, an alternative link is: https://www.bilibili.com/video/BV1Ph411c7ij/?spm_id_from=333.788.recommend_more_video.-1&vd_source=052ff6e1ca06b197e00a9a80affeda05.

The June HUPOST is now available.  Many updates this month, including important upcoming congress deadlines, ECR updates, ETC news....and much more!

The C-HPP is holding a workshop prior to the HUPO 2023 Congress in Busan, Korea at the Centum Premier Hotel in the "Chelsea and Liverpool rooms" on Sunday, 17th September, 09:30 –15:00.

Those who would like to be present are asked to register for free - the sign up sheet is here.

Please pass this onto your students and colleagues who might be attending.

Agenda

09:30 Meet and Greet coffee/tea

10:00-12:00 Session 1 

Welcome, quick Chromosome Team updates:

• neXtProt, human proteome numbers from the 2023-04-18 release (Lydie Lane, Eric Deutsch, Nuno Banderia),
• HPP (Cecilia Lindskog)
• JPR Special Issue (Chris Overall)
• Other business from matters arising from the PIC.
• Special presentation on “Chemoproteomics as an enabling technology for the aims of the C-HPP for PTM, MPs or CP50 research” by Ho Jeong Kwon, Director, Chemical Genomics Leader Research Initiative, Yonsei University, President-Elect, Korean Society for Biochemistry and Molecular Biology (KSBMB).

12:00 - 13:00 Lunch

13:00 Session 2: Future Aims and plans for the C-HPP/HPP and neXtProt

Discussions will include new directions for the C-HPP with an action plan for Human Proteome PTM, MPs, and CP50 (as part of the Grand Challenge) incorporating neXtProt.

15:00 Meeting closes

(15:30 HUPO Council)